Genetic Variant C17orf99:c.70+17G>A (chr17-78146928-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001163075.2(C17orf99):c.70+17G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 1,548,598 control chromosomes in the GnomAD database, including 161,476 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.45 ( 15865 hom., cov: 32)

Exomes 𝑓: 0.45 ( 145611 hom. )

Consequence

C17orf99
NM_001163075.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.36

Publications

13 publications found

Variant links:

Genes affected

C17orf99 (HGNC:34490): (chromosome 17 open reading frame 99) Predicted to enable transmembrane signaling receptor activity. Predicted to be involved in cell surface receptor signaling pathway; mature B cell differentiation involved in immune response; and positive regulation of immunoglobulin production in mucosal tissue. Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

C17orf99 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C17orf99	NM_001163075.2 link	c.70+17G>A		intron_variant	Intron 2 of 4	ENST00000340363.10	NP_001156547.1	Q6UX52

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
C17orf99	ENST00000340363.10 link	c.70+17G>A	intron_variant	Intron 2 of 4	1	NM_001163075.2	ENSP00000343493.4	Q6UX52
C17orf99	ENST00000591995.1 link	c.58+17G>A	intron_variant	Intron 1 of 2	4		ENSP00000466133.1	K7ELL6
C17orf99	ENST00000586999.2 link	n.73+17G>A	intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.450

AC:

68327

AN:

151856

Hom.:

15841

Cov.:

show subpopulations

Gnomad AFR

AF:

0.454

Gnomad AMI

AF:

0.520

Gnomad AMR

AF:

0.382

Gnomad ASJ

AF:

0.560

Gnomad EAS

AF:

0.152

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.491

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.472

Gnomad OTH

AF:

0.475

GnomAD2 exomes

AF:

0.424

AC:

65592

AN:

154790

AF XY:

0.431

show subpopulations

Gnomad AFR exome

AF:

0.455

Gnomad AMR exome

AF:

0.291

Gnomad ASJ exome

AF:

0.567

Gnomad EAS exome

AF:

0.165

Gnomad FIN exome

AF:

0.479

Gnomad NFE exome

AF:

0.478

Gnomad OTH exome

AF:

0.451

GnomAD4 exome

AF:

0.451

AC:

629588

AN:

1396624

Hom.:

145611

Cov.:

AF XY:

0.453

AC XY:

311752

AN XY:

688870

show subpopulations

African (AFR)

AF:

0.463

AC:

14600

AN:

31538

American (AMR)

AF:

0.296

AC:

10571

AN:

35680

Ashkenazi Jewish (ASJ)

AF:

0.564

AC:

14186

AN:

25154

East Asian (EAS)

AF:

0.129

AC:

4599

AN:

35726

South Asian (SAS)

AF:

0.441

AC:

34873

AN:

79132

European-Finnish (FIN)

AF:

0.483

AC:

23795

AN:

49240

Middle Eastern (MID)

AF:

0.598

AC:

3397

AN:

5682

European-Non Finnish (NFE)

AF:

0.462

AC:

497061

AN:

1076554

Other (OTH)

AF:

0.458

AC:

26506

AN:

57918

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

15031

30063

45094

60126

75157

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14804

29608

44412

59216

74020

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.450

AC:

68403

AN:

151974

Hom.:

15865

Cov.:

AF XY:

0.448

AC XY:

33252

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.454

AC:

18816

AN:

41446

American (AMR)

AF:

0.382

AC:

5839

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.560

AC:

1944

AN:

3472

East Asian (EAS)

AF:

0.151

AC:

781

AN:

5162

South Asian (SAS)

AF:

0.441

AC:

2123

AN:

4810

European-Finnish (FIN)

AF:

0.491

AC:

5200

AN:

10584

Middle Eastern (MID)

AF:

0.650

AC:

191

AN:

294

European-Non Finnish (NFE)

AF:

0.472

AC:

32032

AN:

67920

Other (OTH)

AF:

0.479

AC:

1004

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1911

3823

5734

7646

9557

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

624

1248

1872

2496

3120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.467

Hom.:

28831

Bravo

AF:

0.441

Asia WGS

AF:

0.319

AC:

1111

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.0030

(source)

DANN

Benign

0.63

PhyloP100

-4.4

PromoterAI

0.034

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over